Mercurial > repos > bgruening > glimmer_gene_calling_workflow

changeset 5:2405efd751a0 draft

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Uploaded
author bgruening
date Mon, 12 Aug 2013 12:56:19 -0400
parents 22bfc027a718
children 9d5515db5920
files glimmer3_with_trainingset.ga
diffstat 1 files changed, 22 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/glimmer3_with_trainingset.ga	Mon Aug 12 12:08:47 2013 -0400
+++ b/glimmer3_with_trainingset.ga	Mon Aug 12 12:56:19 2013 -0400
@@ -17,8 +17,8 @@
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 283, 
-                "top": 376
+                "left": 235.60880279541016, 
+                "top": 214.3896484375
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -40,8 +40,8 @@
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 443, 
-                "top": 232
+                "left": 454.55167388916016, 
+                "top": 215.35415649414062
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -68,13 +68,19 @@
                 }
             ], 
             "position": {
-                "left": 503, 
-                "top": 486
+                "left": 456.9629592895508, 
+                "top": 555.8248291015625
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActionoutfile": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outfile"
+                }
+            }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2", 
-            "tool_state": "{\"__page__\": 0, \"depth\": \"\\\"7\\\"\", \"period\": \"\\\"3\\\"\", \"width\": \"\\\"12\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"no_stops\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"7\\\"\", \"period\": \"\\\"3\\\"\", \"width\": \"\\\"12\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"no_stops\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}", 
             "tool_version": "0.2", 
             "type": "tool", 
             "user_outputs": []
@@ -109,19 +115,19 @@
                 }
             ], 
             "position": {
-                "left": 674, 
-                "top": 319
+                "left": 696.1604690551758, 
+                "top": 341.2222137451172
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2", 
-            "tool_state": "{\"extend\": \"\\\"False\\\"\", \"__page__\": 0, \"linear\": \"\\\"True\\\"\", \"detailed_report\": \"\\\"False\\\"\", \"seq_input\": \"null\", \"gc_percent\": \"\\\"0.0\\\"\", \"start_codons\": \"\\\"atg,gtg,ttg\\\"\", \"threshold\": \"\\\"30\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"max_olap\": \"\\\"50\\\"\", \"no_indep\": \"\\\"False\\\"\", \"gene_len\": \"\\\"90\\\"\", \"report\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"icm_input\": \"null\"}", 
+            "tool_state": "{\"extend\": \"\\\"False\\\"\", \"__page__\": 0, \"linear\": \"\\\"True\\\"\", \"detailed_report\": \"\\\"False\\\"\", \"seq_input\": \"null\", \"__rerun_remap_job_id__\": null, \"gc_percent\": \"\\\"0.0\\\"\", \"start_codons\": \"\\\"atg,gtg,ttg\\\"\", \"threshold\": \"\\\"30\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"max_olap\": \"\\\"50\\\"\", \"no_indep\": \"\\\"False\\\"\", \"gene_len\": \"\\\"90\\\"\", \"report\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"icm_input\": \"null\"}", 
             "tool_version": "0.2", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "4": {
-            "annotation": "", 
+            "annotation": "We expect our input sequences to have a trailing stop codon, but do not want the star character in the protein output.", 
             "id": 4, 
             "input_connections": {
                 "input1": {
@@ -138,16 +144,16 @@
                 }
             ], 
             "position": {
-                "left": 988, 
-                "top": 351
+                "left": 981.725227355957, 
+                "top": 212.04936981201172
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", 
-            "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"null\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"11\\\"\", \"alternative\": \"\\\"no\\\"\"}", 
+            "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"null\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"yes\\\"\", \"table\": \"\\\"11\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "5.0.0", 
             "type": "tool", 
             "user_outputs": []
         }
     }
-}
+}
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